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Receptor
PDB id Resolution Class Description Source Keywords
4URN 2.3 Å EC: 5.99.1.- CRYSTAL STRUCTURE OF STAPH PARE 24KDA IN COMPLEX WITH NOVOBI STAPHYLOCOCCUS AUREUS ISOMERASE ANTIBIOTICS GYRASE NATURAL PRODUCT
Ref.: STRUCTURES OF KIBDELOMYCIN BOUND TO STAPHYLOCOCCUS GYRB AND PARE SHOWED A NOVEL U-SHAPED BINDING MODE. ACS CHEM.BIOL. V. 9 2023 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NOV C:2000;
B:2000;
A:2000;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
612.624 C31 H36 N2 O11 Cc1c(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4URN 2.3 Å EC: 5.99.1.- CRYSTAL STRUCTURE OF STAPH PARE 24KDA IN COMPLEX WITH NOVOBI STAPHYLOCOCCUS AUREUS ISOMERASE ANTIBIOTICS GYRASE NATURAL PRODUCT
Ref.: STRUCTURES OF KIBDELOMYCIN BOUND TO STAPHYLOCOCCUS GYRB AND PARE SHOWED A NOVEL U-SHAPED BINDING MODE. ACS CHEM.BIOL. V. 9 2023 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4URN - NOV C31 H36 N2 O11 Cc1c(ccc2c....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 4URN - NOV C31 H36 N2 O11 Cc1c(ccc2c....
2 4LP0 ic50 < 10 nM 1YM C18 H14 F3 N5 O3 S CCNC(=O)Nc....
3 4EMV ic50 = 0.005 uM 0R9 C20 H15 F3 N6 O3 CCNC(=O)c1....
4 4MB9 - 28F C18 H20 N6 O3 S CCNC(=O)Nc....
5 4MBC - 28G C21 H24 N6 O3 S C=CCNC(=O)....
6 4LPB ic50 < 10 nM 1YP C19 H14 F3 N7 O3 S CCNC(=O)Nc....
7 4MOT - 2B7 C20 H23 N5 O2 S CC(C)CCN1c....
8 4EM7 ic50 = 7.7 uM 0RA C16 H14 N2 O2 c1cc(cc(c1....
50% Homology Family (50)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4URL ic50 = 500 nM XAM C44 H60 Cl2 N4 O14 Cc1c(c(c([....
2 5CTW - 55D C9 H12 N2 O2 S CCCC(=O)Nc....
3 5CTU - 54X C10 H6 N2 O S2 c1cc(sc1)c....
4 3U2D - 08B C16 H18 Br N5 O3 Cc1c(cc([n....
5 5CTX ic50 = 1.32 uM 55G C20 H13 N5 O S c1ccc(cc1)....
6 3TTZ ic50 = 0.004 uM 07N C15 H15 Cl2 F N4 O3 S Cc1c(c(c([....
7 5D6Q ic50 = 5.8 uM 57V C17 H17 N5 O S CCNC(=O)Nc....
8 3U2K - 087 C17 H18 Cl3 N5 O2 Cc1c(c(c([....
9 5D6P ic50 = 2.5 uM 57U C11 H14 N4 O2 S CCNC(=O)Nc....
10 5Z9P - AX7 C7 H7 N3 c1ccc2c(c1....
11 5D7C ic50 = 0.14 uM 57W C20 H18 N6 O CCNC(=O)Nc....
12 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
13 4WUB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
14 4PRX - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
15 4XTJ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
16 1EI1 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
17 4PU9 - ADP BEF n/a n/a
18 4WUC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
19 4PRV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
20 4WUD - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
21 4ZVI Kd = 0.47 uM 4S4 C14 H11 Br2 N3 O4 c1cc(ccc1C....
22 1S16 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
23 4URN - NOV C31 H36 N2 O11 Cc1c(ccc2c....
24 4HY1 Ki = 2 nM 19X C20 H19 Cl N6 O S CCc1c(c2c(....
25 4HYM Ki = 6 nM CJC C19 H19 Cl N8 O S CCc1c(c2c(....
26 4HXW Ki = 2 nM 1A0 C19 H19 Cl N8 S CCc1c(c2c(....
27 4GFN Ki = 5 nM SUY C17 H18 Cl N7 S CCc1c(c2c(....
28 4P8O - 883 C19 H16 F N7 O CCNC(=O)Nc....
29 1KIJ - NOV C31 H36 N2 O11 Cc1c(ccc2c....
30 4B6C ic50 = 0.69 uM B5U C27 H34 N6 O2 Cc1ccc(cc1....
31 4EMV ic50 = 0.005 uM 0R9 C20 H15 F3 N6 O3 CCNC(=O)c1....
32 4MB9 - 28F C18 H20 N6 O3 S CCNC(=O)Nc....
33 4MBC - 28G C21 H24 N6 O3 S C=CCNC(=O)....
34 4LPB ic50 < 10 nM 1YP C19 H14 F3 N7 O3 S CCNC(=O)Nc....
35 4MOT - 2B7 C20 H23 N5 O2 S CC(C)CCN1c....
36 4EM7 ic50 = 7.7 uM 0RA C16 H14 N2 O2 c1cc(cc(c1....
37 5Z9Q - HX4 C9 H9 N3 c1ccc(cc1)....
38 5Z4H - AX7 C7 H7 N3 c1ccc2c(c1....
39 5Z9L - 8H8 C7 H4 F N O c1cc(c(cc1....
40 5Z9E - AX7 C7 H7 N3 c1ccc2c(c1....
41 1KZN Kd = 1.2 nM CBN C35 H37 Cl N2 O11 Cc1ccc([nH....
42 1AJ6 Kd = 1.2 uM NOV C31 H36 N2 O11 Cc1c(ccc2c....
43 5Z9B - AX7 C7 H7 N3 c1ccc2c(c1....
44 5MMO - 9JG C22 H21 N5 O3 CCNC(=O)Nc....
45 5Z4O - HX8 C12 H10 O2 c1ccc(cc1)....
46 5MMP ic50 = 0.03 uM G3Z C22 H20 N6 O CCNC(=O)Nc....
47 4DUH Kd = 6.6 uM RLI C17 H16 N4 O3 S2 CCC(=O)Nc1....
48 5MMN ic50 = 0.125 uM O54 C19 H20 N4 O CCNC(=O)Nc....
49 5Z9F - AX7 C7 H7 N3 c1ccc2c(c1....
50 4BAE ic50 = 3 nM RWX C19 H21 Br Cl N7 O4 S Cc1c(c(c([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NOV; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 NOV 1 1
2 CBN 0.669291 0.820895
3 CZJ 0.637931 0.901639
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4URN; Ligand: NOV; Similar sites found with APoc: 277
This union binding pocket(no: 1) in the query (biounit: 4urn.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 4TV1 36M None
2 6B5Q PPI CZS 2KY MLY 1XY None
3 2B4D COA None
4 1H0A I3P None
5 5WGD EST None
6 5WGQ EST None
7 5DXE EST None
8 3UUD EST None
9 2QA8 GEN None
10 4TUZ 36J None
11 4MG8 27J None
12 2QZO KN1 None
13 4MGB XDH None
14 1NZY BCA None
15 4MGD 27N None
16 2HJ3 FAD None
17 4MG7 27H None
18 2BJ4 OHT None
19 4MGA 27L None
20 4XCL AGS 1.33333
21 4URF 1PS 1.33333
22 3L0E G58 1.33333
23 3SFI 3SF 1.33333
24 5HYR EST 1.33333
25 1BOB ACO 1.5625
26 4R57 ACO 1.70455
27 2G86 UMP 1.77778
28 3KP6 SAL 1.98676
29 3MBG FAD 2.15827
30 1BGQ RDC 2.22222
31 1IZE IVA VAL VAL STA ALA STA 2.22222
32 3KFC 61X 2.22222
33 6B21 C9V 2.22222
34 5TUX ECH 2.22222
35 5AAV GW5 2.22222
36 5N2I NAP 2.22222
37 4DK7 0KS 2.22222
38 3U5S FAD 2.38095
39 3O55 FAD 2.4
40 3KA2 2NC 2.46305
41 2CNT COA 2.5
42 1WWZ ACO 2.51572
43 1JR8 FAD 2.5641
44 4G86 BNT 2.66667
45 5FM0 WAQ 2.66667
46 1GNI OLA 2.66667
47 5CJH 522 2.66667
48 1XAP TTB 2.66667
49 4RHE FMN 2.66667
50 5HWO HMG 2.66667
51 5K53 STE 2.66667
52 5KOR GDP 2.66667
53 6CB2 OLC 3.11111
54 4Y9J UCC 3.11111
55 3GYT DL4 3.11111
56 3UR0 SVR 3.11111
57 6F6E PLM 3.11111
58 2WPW ACO 3.11111
59 2E2R 2OH 3.11111
60 3LDW ZOL 3.11111
61 4RC8 STE 3.15315
62 2VZZ SCA 3.21101
63 1UVC STE 3.2967
64 4IVG ANP 3.55556
65 6ARJ BW4 3.55556
66 5ICK FEZ 3.55556
67 6ARJ SAH 3.55556
68 3LLI FAD 3.55556
69 3L9R L9R 3.55556
70 3BQ5 HCS 3.55556
71 3RUU 37G 3.55556
72 4OIV XX9 3.55556
73 2O3Z AI7 3.55556
74 3BEJ MUF 3.55556
75 4KOT CE3 3.7037
76 4RI1 ACO 3.76344
77 3E85 BSU 3.79747
78 1TIQ COA 3.88889
79 2HFN FMN 3.92157
80 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 4
81 4B5P ACO 4
82 3DST GRG 4
83 2H6T IVA VAL VAL STA ALA STA 4
84 1ZAP A70 4
85 1UDY FAD 4
86 3G9E RO7 4
87 1UDY CS8 4
88 2P4Y C03 4
89 5TWO 7MV 4
90 1XAJ NAD 4
91 1XAJ CRB 4
92 2GWH PCI 4
93 2IID PHE 4
94 2IID FAD 4
95 3FUR Z12 4
96 3OKI OKI 4
97 2HFP NSI 4
98 1X0P FAD 4.1958
99 3JUQ AJD 4.32432
100 3JUQ AKD 4.32432
101 5N26 CPT 4.3956
102 2IOR ADP 4.44444
103 4Q0A 4OA 4.44444
104 5U5G 7VD 4.44444
105 4MRP GSH 4.44444
106 3PMA SCR 4.44444
107 1I58 ADP 4.7619
108 1I58 ACP 4.7619
109 1NF8 BOG 4.83092
110 4BIX ADP 4.88889
111 5HGR 45D 4.88889
112 2JJK R15 4.88889
113 1TV5 N8E 4.88889
114 1ZSQ PIB 4.88889
115 2AX9 BHM 4.88889
116 5B4B LP5 4.88889
117 5MWY YNU 4.88889
118 5HCV 60R 4.88889
119 4UDB CV7 4.88889
120 4XPL ACO 4.90798
121 5XS3 VAL ARG SER ARG ARG CYS LEU ARG LEU 5.10204
122 3KPE TM3 5.12821
123 3WHB DCC 5.15464
124 2BHW NEX 5.33333
125 1ZED PNP 5.33333
126 3QCP FAD 5.33333
127 1TMX HGX 5.33333
128 1DB1 VDX 5.33333
129 3OLL EST 5.33333
130 2YJD YJD 5.33333
131 1U3R 338 5.33333
132 1M13 HYF 5.33333
133 1YYE 196 5.33333
134 5YFT RI2 5.33333
135 2NP9 YE1 5.33333
136 5FVJ ACO 5.42169
137 5I8F ML1 5.45455
138 3EHH ADP 5.50459
139 3FV3 IVA VAL VAL STA ALA STA 5.60472
140 2D5X L35 5.67376
141 4XU6 TDA 5.71429
142 2HHP FLC 5.77778
143 5OF9 ANP 5.77778
144 5FB3 NDP 5.77778
145 5ECP MET 5.77778
146 5ECP JAA 5.77778
147 5ECP ATP 5.77778
148 1ZDU P3A 5.77778
149 5IBE 69M 5.77778
150 2GGH NLQ 5.77778
151 4WGF HX2 5.85366
152 1ID0 ANP 5.92105
153 5LLT DND 6.10329
154 3FEI CTM 6.22222
155 4TXJ THM 6.22222
156 1XX4 BAM 6.22222
157 2Q1H AS4 6.22222
158 5APK 76E 6.22222
159 4G9N NGA 6.29371
160 4KVX ACO 6.41026
161 2Q4V ACO 6.47059
162 1MID LAP 6.59341
163 3ITJ CIT 6.66667
164 4V3I ASP LEU THR ARG PRO 6.66667
165 1KOL NAD 6.66667
166 2ZPA ACO 6.66667
167 5TPR NAD 6.66667
168 3K9U ACO 6.91824
169 3LF0 ATP 7.01754
170 3LN0 52B 7.11111
171 2KCE D16 7.11111
172 3U3U EAH 7.11111
173 1SR7 MOF 7.11111
174 4JZX 476 7.11111
175 4GFD 0YB 7.31707
176 1WPQ NAD 7.55556
177 3GWN FAD 7.89474
178 4IPE ANP 8
179 4UA3 COA 8.24742
180 3IPQ 965 8.44444
181 5FPN KYD 8.44444
182 4POJ 2VP 8.44444
183 6A5Y 9R0 8.44444
184 4M8E 29V 8.44444
185 3FAL LO2 8.44444
186 3NRR UMP 8.44444
187 3NRR D16 8.44444
188 3TDC 0EU 8.88889
189 4QC6 30N 8.93855
190 4H6U ACO 9
191 2VBQ BSJ 9.09091
192 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 9.18367
193 1SJD NPG 9.33333
194 4R6W PC 9.33333
195 2VL8 CTS 9.33333
196 1X87 NAD 9.33333
197 5BNS 4VM 9.33333
198 5GK9 ACO 9.33333
199 5O4J SAH 9.33333
200 5O4J PJL 9.33333
201 3EHG ATP 9.375
202 1JGS SAL 9.42029
203 5IDM ANP 9.49721
204 5EK3 5PK 9.77778
205 4LO2 GAL BGC 9.77778
206 3ORF NAD 9.77778
207 1UHK CZN 9.94764
208 5JHD GLY ILE LEU GLY PHE VAL PHE THR LEU 10
209 6GH1 ARG LEU PRO ALA LYS ALA PRO LEU LEU 10
210 5WL1 D3D 10.101
211 5WL1 CUY 10.101
212 3DBX PLM 10.101
213 5U98 1KX 10.101
214 6BJ3 ILE PRO LEU THR GLU GLU ALA GLU LEU 10.101
215 5U98 VAL THR THR ASP ILE GLN VAL LYS VAL 10.101
216 5ISZ GLY ILE LEU GLY PHE VAL PHE THR LEU 10.2041
217 3H4L ANP 10.2222
218 6D28 NEC 10.2222
219 2WR1 NAG 10.2222
220 2GFD RDA 10.2222
221 5HH0 COA 10.2222
222 5K04 COA 10.2222
223 4PJT 2YQ 10.2222
224 4XNV BUR 10.2222
225 1B63 ANP 10.6667
226 6DIO CIT 10.6667
227 5O3Q CMP 10.8333
228 3RUG DB6 11.1111
229 4OGQ 7PH 11.1628
230 6GMN F4E 11.5385
231 4XOQ F42 11.5942
232 3WR7 COA 11.7647
233 1Y8O ADP 12
234 1YMT DR9 12
235 1KOR ARG 12
236 3PF7 MLA 12
237 4NB5 2JT 12.2807
238 1T0S BML 12.7907
239 2ZKJ ADP 12.8889
240 5ZM0 FAD 12.8889
241 1XVB 3BR 12.8889
242 3GWL FAD 13.2075
243 6GL8 F3Q 13.3721
244 2C2A ADP 13.7778
245 4GCZ ADP 14.2222
246 2VCH UDP 14.2222
247 4RW3 TDA 14.6667
248 4RW3 PLM 14.6667
249 2W3L DRO 15.2778
250 4B7P 9UN 15.5556
251 2NU8 COA 15.5556
252 3RMK BML 15.6627
253 2HKJ RDC 16
254 2O1V ADP 16.4444
255 3NT6 COA 16.8889
256 3NTA COA 16.8889
257 1YC4 43P 17.3333
258 2YI0 YI0 17.3333
259 3NTD COA 17.3333
260 5UC4 83S 18.1818
261 1OQC FAD 18.4
262 1GKZ ADP 18.6667
263 3K60 ADP 19.5556
264 5DEY 59T 19.5556
265 2XCM ADP 20.4444
266 5J6A P46 20.8889
267 1GHE ACO 21.4689
268 1TH8 ADP 22.069
269 3D36 ADP 22.1311
270 4V1F BQ1 23.2558
271 5F5R ANP 23.5556
272 5Y3N 8MF 23.5556
273 1TID ATP 24.2647
274 4WAS COO 27.1111
275 1QZR CDX 40
276 1QZR ANP 40
277 1ZXM ANP 43.1111
Pocket No.: 2; Query (leader) PDB : 4URN; Ligand: NOV; Similar sites found with APoc: 91
This union binding pocket(no: 2) in the query (biounit: 4urn.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 6CHP F0Y None
2 4Q1A 2XZ 0.888889
3 4Q1A UDP 0.888889
4 5M37 9SZ 1.77778
5 3QDC RET 1.77778
6 2IYF UDP 1.77778
7 6C28 WCA 2.15054
8 3T58 FAD 2.22222
9 3WGT FAD 2.22222
10 3WGT QSC 2.22222
11 4WOP CTP 2.22222
12 4JJF FE9 2.22222
13 4IBF 1D5 2.32558
14 2QZX IVA VAL VAL STA ALA STA 2.33918
15 4M0R 644 2.63852
16 5GWT SIN 2.66667
17 5EXW 7DT 2.66667
18 3UP3 XCA 2.66667
19 5B0I BOG 2.66667
20 2VAR ANP 2.66667
21 2CIX CEJ 2.66667
22 5CFT APC 2.7027
23 5CFT 51G 2.7027
24 5X3R 7Y3 2.92683
25 2ZWA SAH 3.11111
26 2WK1 SAH 3.11111
27 3QKT ANP 3.11111
28 4ZBR DIF 3.11111
29 4ZBR NPS 3.11111
30 1I00 D16 3.11111
31 1I00 UMP 3.11111
32 4ZVV GN0 3.55556
33 4ZVV NAD 3.55556
34 1RYI FAD 3.55556
35 1IK4 PGH 3.94737
36 2X1L ADN 4
37 1FCH TYR GLN SER LYS LEU 4
38 5BNW 12V 4
39 5HVA DUP 4.28571
40 1RJD SAM 4.44444
41 3VRV YSD 4.44444
42 2Z7I 742 4.44444
43 5LGA 6VH 4.44444
44 4Q0A GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 4.44444
45 3MMR ABH 4.44444
46 1LW4 TLP 4.88889
47 3V49 PK0 4.88889
48 5L7G 6QE 4.88889
49 2A3I C0R 4.88889
50 4I4B 1CV 5.33333
51 2I0G I0G 5.33333
52 5K7H IVC 5.33333
53 3O3O 2RH 5.33333
54 3VPH FBP 5.33333
55 3V1V GST 5.77778
56 5N8V KZZ 5.7971
57 2J9D ADP 5.88235
58 5NM7 GLY 6.01504
59 6MPT C30 6.22222
60 3N7O N7O 6.22222
61 3SP6 IL2 6.22222
62 3OV6 MK0 6.66667
63 3P0K FAD 7.11111
64 5XET ME8 7.11111
65 3VZ3 NAP 7.55556
66 3FAL REA 8.44444
67 1FM9 9CR 8.44444
68 4XB4 45D 8.55263
69 3WDM ADN 8.88889
70 3W54 RNB 8.88889
71 4QVX 3CQ 8.98204
72 4X6F 3XU 9.52381
73 4L2I NAD 9.77778
74 4L2I FAD 9.77778
75 1Q19 APC 9.77778
76 3QFJ LEU LEU PHE GLY PHE PRO VAL TYR VAL 10
77 5T70 THR SER ASN LEU GLN GLU GLN ILE GLY TRP 10.101
78 5C9J STE 10.101
79 5HGZ ACO 10.2222
80 5KBZ 3B2 10.2222
81 2YYE APC 12.4444
82 3AXB PRO 12.8889
83 4LSJ LSJ 13.7778
84 5G5W R8C 13.7778
85 4P6X HCY 13.7778
86 1M2Z DEX 13.7778
87 3BQD DAY 13.7778
88 3ZOK NAD 14.2222
89 4CRZ ACO 15.3846
90 5LS7 ACO 15.6863
91 1FO0 ILE ASN PHE ASP PHE ASN THR ILE 16.3793
Pocket No.: 3; Query (leader) PDB : 4URN; Ligand: NOV; Similar sites found with APoc: 30
This union binding pocket(no: 3) in the query (biounit: 4urn.bio3) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 5ET3 60C None
2 3FSM 2NC 2.46305
3 3EMY IVA VAL VAL STA ALA STA 3.11111
4 5XDT MB3 3.11111
5 5XDT GDP 3.11111
6 1GJW GLC 3.55556
7 2ZRU FMN 3.55556
8 5Z2L NDP 4
9 6CEP OXM 4
10 4ZUL UN1 4.44444
11 4ETZ C2E 4.7138
12 4X8D AVI 4.88889
13 1R6T TYM 5.33333
14 6BA2 7KM 5.76271
15 4MNS 2AX 5.77778
16 5I39 FAD 5.77778
17 3Q9T FAY 5.77778
18 1OYJ GSH 6.22222
19 1DTL BEP 6.8323
20 2XN3 ID8 7.11111
21 3AB1 FAD 7.11111
22 1LTH NAD 7.55556
23 4XYM COA 8.44444
24 3ZUY TCH 8.88889
25 3E70 GDP 8.88889
26 4WJT NAG 9.58084
27 4OGQ UMQ 11.1628
28 1GZ4 ATP 12.4444
29 4IAE 1DX 13.2275
30 5N5U AMP 14.2222
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